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Structure paper

TitleEnergy barriers and driving forces in tRNA translocation through the ribosome.
Journal, issue, pagesNat Struct Mol Biol, Vol. 20, Issue 12, Page 1390-1396, Year 2013
Publish dateNov 3, 2013
AuthorsLars V Bock / Christian Blau / Gunnar F Schröder / Iakov I Davydov / Niels Fischer / Holger Stark / Marina V Rodnina / Andrea C Vaiana / Helmut Grubmüller /
PubMed AbstractDuring protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics ...During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM data. Resolving fast transitions between states, we find that tRNA motions govern the transition rates within the pre- and post-translocation states. Intersubunit rotations and L1-stalk motion exhibit fast intrinsic submicrosecond dynamics. The L1 stalk drives the tRNA from the peptidyl site and links intersubunit rotation to translocation. Displacement of tRNAs is controlled by 'sliding' and 'stepping' mechanisms involving conserved L16, L5 and L1 residues, thus ensuring binding to the ribosome despite large-scale tRNA movement. Our results complement structural data with a time axis, intrinsic transition rates and molecular forces, revealing correlated functional motions inaccessible by other means.
External linksNat Struct Mol Biol / PubMed:24186064
MethodsEM (single particle)
Resolution9 - 20.0 Å
Structure data

2472

4v6z

EMDB-2472: Energy barriers and driving forces of tRNA translocation through the ribosome
PDB-4v6z: E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1b)
Method: EM (single particle) / Resolution: 12.0 Å

2473

4v73

EMDB-2473: Energy barriers and driving forces of tRNA translocation through the ribosome
PDB-4v73: E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5a)
Method: EM (single particle) / Resolution: 15.0 Å

2474

4v77

EMDB-2474: Energy barriers and driving forces of tRNA translocation through the ribosome
PDB-4v77: E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2b)
Method: EM (single particle) / Resolution: 17.0 Å

2475

4v78

EMDB-2475: Energy barriers and driving forces of tRNA translocation through the ribosome
PDB-4v78: E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3a)
Method: EM (single particle) / Resolution: 20.0 Å

PDB-4v6y:
E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1a)
Method: ELECTRON MICROSCOPY / Resolution: 12 Å

PDB-4v70:
E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre3)
Method: ELECTRON MICROSCOPY / Resolution: 17 Å

PDB-4v71:
E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre2)
Method: ELECTRON MICROSCOPY / Resolution: 20 Å

PDB-4v72:
E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre4)
Method: ELECTRON MICROSCOPY / Resolution: 13 Å

PDB-4v74:
70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5b)
Method: ELECTRON MICROSCOPY / Resolution: 17 Å

PDB-4v75:
E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic post-translocation state (post1)
Method: ELECTRON MICROSCOPY / Resolution: 12 Å

PDB-4v76:
E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2a)
Method: ELECTRON MICROSCOPY / Resolution: 17 Å

PDB-4v79:
E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3b)
Method: ELECTRON MICROSCOPY / Resolution: 15 Å

PDB-4v7a:
E. coli 70S-fMetVal-tRNAVal post-translocation complex (post4)
Method: ELECTRON MICROSCOPY / Resolution: 9 Å

Chemicals

ChemComp-VAL:
VALINE

ChemComp-FME:
N-FORMYLMETHIONINE

Source
  • escherichia coli (E. coli)
  • synthetic construct (others)
KeywordsRIBOSOME / cryo-EM refinement / tRNA / translocation intermediate

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